diff --git a/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index 0c4619259b231540b585fb3d028b482ebaf4945d..930c8b73b8c96ed7a8e12c738c6d59aad5357def 100644
--- a/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -7,7 +7,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.apps.{BedToInterval, BiopetFlagstat}
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.function.bedtools.{BedtoolsCoverage, BedtoolsIntersect}
-import nl.lumc.sasc.biopet.function.picard.{CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics}
+import nl.lumc.sasc.biopet.function.picard.{CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics}
import nl.lumc.sasc.biopet.function.samtools.SamtoolsFlagstat
class BamMetrics(val root:Configurable) extends QScript with BiopetQScript {
@@ -36,6 +36,7 @@ class BamMetrics(val root:Configurable) extends QScript with BiopetQScript {
add(BiopetFlagstat(this, inputBam, outputDir))
add(CollectGcBiasMetrics(this, inputBam, outputDir))
add(CollectInsertSizeMetrics(this, inputBam, outputDir))
+ add(CollectAlignmentSummaryMetrics(this, inputBam, outputDir))
val baitIntervalFile = if (baitBedFile != null) new File(outputDir, baitBedFile.getName.stripSuffix(".bed") + ".interval") else null
if (baitIntervalFile != null)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 5dd12235104741a8bef43ded1f40520d6bc966f2..1444720854e34cc459a458bab1185e359c42b4fc 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -22,8 +22,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
var vmem: String = _
val defaultVmem: String = ""
- @Argument(doc="Executeble")
- var executeble: String = _
+ @Argument(doc="Executable")
+ var executable: String = _
protected def beforeCmd {
}
@@ -32,7 +32,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
}
override def freezeFieldValues() {
- checkExecuteble
+ checkExecutable
afterGraph
jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + analysisName + ".out")
@@ -49,26 +49,26 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
super.freezeFieldValues()
}
- protected def checkExecuteble {
- try if (executeble != null) {
+ protected def checkExecutable {
+ try if (executable != null) {
val buffer = new StringBuffer()
- val cmd = Seq("which", executeble)
+ val cmd = Seq("which", executable)
val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
if (process.exitValue == 0) {
- executeble = buffer.toString
- val file = new File(executeble)
- executeble = file.getCanonicalPath
+ executable = buffer.toString
+ val file = new File(executable)
+ executable = file.getCanonicalPath
} else {
- logger.error("executeble: '" + executeble + "' not found, please check config")
- throw new QException("executeble: '" + executeble + "' not found, please check config")
+ logger.error("executable: '" + executable + "' not found, please check config")
+ throw new QException("executable: '" + executable + "' not found, please check config")
}
} catch {
- case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executeble skipped: " + ioe)
+ case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
}
}
final protected def preCmdInternal {
- checkExecuteble
+ checkExecutable
//for (input <- this.inputs) if (!input.exists) throw new IllegalStateException("Input: " + input + " for " + analysisName + " is missing")
//logger.debug("Config for " + analysisName + ": " + localConfig)
@@ -96,7 +96,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
case _ =>
}
}
- logger.warn("Version command: '" + versionCommand + "' give a exit code " + process.exitValue + " but no version was found, executeble oke?")
+ logger.warn("Version command: '" + versionCommand + "' give a exit code " + process.exitValue + " but no version was found, executable oke?")
return "N/A"
}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index 1109bbb009d6a6e08fca248d85f969907ad21093..543d9450474b4eace2b36b737315fa02b7f6e3c9 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -3,12 +3,12 @@ package nl.lumc.sasc.biopet.core
import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
abstract class BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
- executeble = "java"
+ executable = "java"
override def commandLine: String = {
preCmdInternal
val cmd = super.commandLine
- val finalCmd = executeble + cmd.substring(cmd.indexOf(" "))
+ val finalCmd = executable + cmd.substring(cmd.indexOf(" "))
// addJobReportBinding("command", cmd)
return cmd
}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala
index bcdcc040f9ac470c82bcbf6964818b04b497016d..497085b543ec309857ba8baec4a50cb2365277fb 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala
@@ -12,9 +12,9 @@ class Cat(val root:Configurable) extends BiopetCommandLineFunction {
@Output(doc="Unzipped file", required=true)
var output: File = _
- executeble = config("exe", "cat")
+ executable = config("exe", "cat")
- def cmdLine = required(executeble) + repeat(input) + " > " + required(output)
+ def cmdLine = required(executable) + repeat(input) + " > " + required(output)
}
object Cat {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
index 424b3109bdaeff85c1419f6aa1fe297f75d1c0ee..52fa44c875921d35c0b25396ab7f84924da94b0b 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala
@@ -13,7 +13,7 @@ class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction {
@Output(doc="Unzipped file")
var output: File = _
- executeble = config("exe", "pbzip2")
+ executable = config("exe", "pbzip2")
var decomrpess = true
var memory: Int = config("memory", 1000)
@@ -25,7 +25,7 @@ class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction {
memory = memory * threads
}
- def cmdLine = required(executeble) +
+ def cmdLine = required(executable) +
conditional(decomrpess, "-d") +
conditional(!decomrpess, "-z") +
optional("-p", threads, spaceSeparated=false) +
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala
index 5eac0f3183ef4489709d520e8c8eec24f9ab8b48..dc347be64d084fdac342afd69a8a1f78ab68d1ec 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala
@@ -10,7 +10,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
@Input(doc="Python script", required=false)
var python_script: File = _
- executeble = config("python_exe", "python")
+ executable = config("python_exe", "python")
protected var python_script_name : String = _
def setPythonScript(script:String) { setPythonScript(script,"") }
@@ -25,6 +25,6 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
}
def getPythonCommand() : String = {
- required(executeble) + required(python_script)
+ required(executable) + required(python_script)
}
}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
index 136a6919ea85685658cf871cb181b2c010346ea6..b8c8a03712d0a5d9fef7f6fa7c90774183b9b4a5 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
@@ -12,7 +12,7 @@ class Sha1sum(val root:Configurable) extends BiopetCommandLineFunction {
@Output(doc="Unzipped file")
var output: File = _
- executeble = config("exe","sha1sum")
+ executable = config("exe","sha1sum")
- def cmdLine = required(executeble) + required(input) + " > " + required(output)
+ def cmdLine = required(executable) + required(input) + " > " + required(output)
}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
index 282aff06fd57de22d9023c3bd5ae426c1fc061fc..931b7183b0af80ed8cb677afbcea87c533bd3894 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
@@ -12,9 +12,9 @@ class Zcat(val root:Configurable) extends BiopetCommandLineFunction {
@Output(doc="Unzipped file")
var output: File = _
- executeble = config("exe", "zcat")
+ executable = config("exe", "zcat")
- def cmdLine = required(executeble) + required(input) + " > " + required(output)
+ def cmdLine = required(executable) + required(input) + " > " + required(output)
}
object Zcat {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/Bedtools.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/Bedtools.scala
index 0f3d8c206037142c2ae72eb0bc21d716f0649421..522bbc1a1e51812cb7d63823b2fb43b58def6372 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/Bedtools.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/Bedtools.scala
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.function.bedtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
abstract class Bedtools extends BiopetCommandLineFunction {
- executeble = config("exe", "bedtools", "bedtools")
- override def versionCommand = executeble + " --version"
+ executable = config("exe", "bedtools", "bedtools")
+ override def versionCommand = executable + " --version"
override val versionRegex = """bedtools (.*)""".r
}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala
index d1e9bef388e6ff2adba04fdc5d58c873b15aa5ea..a6f57ea0edbb0fff73aa2cbcf4e91d4a1f21f3df 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsCoverage.scala
@@ -23,7 +23,7 @@ class BedtoolsCoverage(val root:Configurable) extends Bedtools {
if (input.getName.endsWith(".bam")) inputTag = "-abam"
}
- def cmdLine = required(executeble) + required("coverage") +
+ def cmdLine = required(executable) + required("coverage") +
required(inputTag, input) +
required("-b", intersectFile) +
conditional(depth, "-d") +
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala
index 5cdc9fa1472f3f8821a8e41d1ac2bee1d100e471..8ffa3993db0b4e21c3af6ab6428d72f152fd290e 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/bedtools/BedtoolsIntersect.scala
@@ -26,7 +26,7 @@ class BedtoolsIntersect(val root:Configurable) extends Bedtools {
if (input.getName.endsWith(".bam")) inputTag = "-abam"
}
- def cmdLine = required(executeble) + required("intersect") +
+ def cmdLine = required(executable) + required("intersect") +
required(inputTag, input) +
required("-b", intersectFile) +
required("-f", minOverlap) +
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala
index 8e2c4717d2cb8203754459908eafec49fe65d92b..8016282f14426f40cec125682610be11ca329bb5 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/picard/Picard.scala
@@ -25,7 +25,7 @@ trait Picard extends BiopetJavaCommandLineFunction {
@Argument(doc="CREATE_MD5_FILE", required = false)
var createMd5: Boolean = config("createmd5", false, "picard")
- override def versionCommand = executeble + " " + javaOpts + " " + javaExecutable + " -h"
+ override def versionCommand = executable + " " + javaOpts + " " + javaExecutable + " -h"
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0,1)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/Samtools.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/Samtools.scala
index 816f28304437434e60f4cc6e95c918aa6691e6e1..f362babf20b0018369c7bce9da10e260ff22fd89 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/Samtools.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/Samtools.scala
@@ -3,8 +3,8 @@ package nl.lumc.sasc.biopet.function.samtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
abstract class Samtools extends BiopetCommandLineFunction {
- executeble = config("exe", "samtools", "samtools")
- override def versionCommand = executeble
+ executable = config("exe", "samtools", "samtools")
+ override def versionCommand = executable
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0,1)
}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala
index a469f69ff4cdedfbf2faaf8fc7ab7002ec30e037..53f1eb6e16aafc9f9a48afb216f76faf87a7b872 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/samtools/SamtoolsFlagstat.scala
@@ -11,7 +11,7 @@ class SamtoolsFlagstat(val root:Configurable) extends Samtools {
@Output(doc="output File")
var output: File = _
- def cmdLine = required(executeble) + required("flagstat") + required(input) + " > " + required(output)
+ def cmdLine = required(executable) + required("flagstat") + required(input) + " > " + required(output)
}
object SamtoolsFlagstat {
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
index 7081e36e21d91a0f5b249ff1dcf65cf441f356c1..f00b0c78a0cb3f6bd638aa733c02c069e8bd73aa 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
@@ -17,8 +17,8 @@ class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
@Output(doc="Output fastq file")
var fastq_output: File = _
- executeble = config("exe","cutadapt")
- override def versionCommand = executeble + " --version"
+ executable = config("exe","cutadapt")
+ override def versionCommand = executable + " --version"
override val versionRegex = """(.*)""".r
var default_clip_mode:String = config("default_clip_mode", "3")
@@ -37,7 +37,7 @@ class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
def cmdLine = {
if (!opt_adapter.isEmpty || !opt_anywhere.isEmpty || !opt_front.isEmpty) {
analysisName = getClass.getName
- required(executeble) +
+ required(executable) +
// options
repeat("-a", opt_adapter) +
repeat("-b", opt_anywhere) +
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
index 30d01566f36e51b1be9cdda734a1f0560dd2b71a..630a27de9071d460e6099cd66397f1bf1ad02038 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
@@ -17,7 +17,7 @@ class Fastqc(val root:Configurable) extends BiopetCommandLineFunction {
@Output(doc="Output", shortName="out")
var output: File = _
- executeble = config("exe","fastqc")
+ executable = config("exe","fastqc")
var java_exe: String = config("exe", "java", "java")
var kmers: Int = config("kmers", 5)
var quiet: Boolean = config("quiet", false)
@@ -28,15 +28,15 @@ class Fastqc(val root:Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 4
override def afterGraph {
- this.checkExecuteble
- val fastqcDir = executeble.substring(0, executeble.lastIndexOf("/"))
+ this.checkExecutable
+ val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
if (contaminants == null) contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
}
- override def versionCommand = executeble + " --version"
+ override def versionCommand = executable + " --version"
def cmdLine = {
- required(executeble) +
+ required(executable) +
optional("--java", java_exe) +
optional("--threads",threads) +
optional("--contaminants",contaminants) +
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
index ed0b44608a8a7cfcfead2266edb7878a59d53fca..79af73b5b0a35a9e83cc03f6ef1d0f47c281a9b2 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
@@ -29,7 +29,7 @@ class Sickle(val root:Configurable) extends BiopetCommandLineFunction {
@Output(doc="stats output")
var output_stats: File = null
- executeble = config("exe", "sickle")
+ executable = config("exe", "sickle")
var qualityType: String = config("qualitytype", null)
var defaultQualityType: String = _
@@ -40,14 +40,14 @@ class Sickle(val root:Configurable) extends BiopetCommandLineFunction {
if (qualityType == null && defaultQualityType != null) qualityType = defaultQualityType
}
- override def versionCommand = executeble + " --version"
+ override def versionCommand = executable + " --version"
override def beforeCmd {
qualityType = getQualityTypeFromFile
}
def cmdLine = {
- var cmd: String = required(executeble)
+ var cmd: String = required(executable)
if (input_R2 != null) {
cmd += required("pe") +
required("-r", input_R2) +
diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
index 45705fa97347c188ebc3a9b93acaa004202663e4..8cda591336827de338aba571fa3a3265bafdf189 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
@@ -22,17 +22,17 @@ class Bwa(val root:Configurable) extends BiopetCommandLineFunction {
var RG: String = _
var M: Boolean = config("M", true)
- executeble = config("exe", "bwa")
+ executable = config("exe", "bwa")
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0,1)
override val defaultVmem = "6G"
override val defaultThreads = 8
- override def versionCommand = executeble
+ override def versionCommand = executable
def cmdLine = {
- required(executeble) +
+ required(executable) +
required("mem") +
optional("-t", nCoresRequest) +
optional("-R", RG) +
diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
index c7ef295d56090204449ff7df8871c22cb85d56c3..cf116fbb390c16d1adc8b27ce75f5dadad003244 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
@@ -34,7 +34,7 @@ class Star(val root:Configurable) extends BiopetCommandLineFunction {
@Output(doc="Output SAindex file", required=false)
var outputSAindex: File = _
- executeble = config("exe", "STAR")
+ executable = config("exe", "STAR")
@Argument(doc="Output Directory")
var outputDir: String = _
@@ -64,7 +64,7 @@ class Star(val root:Configurable) extends BiopetCommandLineFunction {
}
def cmdLine : String = {
- var cmd: String = required("cd",outputDir) + "&&" + required(executeble)
+ var cmd: String = required("cd",outputDir) + "&&" + required(executable)
if (runmode != null && runmode == "genomeGenerate") { // Create index
cmd += required("--runMode", runmode) +
required("--genomeFastaFiles", referenceFile)